Hi everyone,

May I ask what is the most updated EPIC V2 chip analysis using minfi package?

Is it still using the annotation provided by jokergoo?

install("jokergoo/IlluminaHumanMethylationEPICv2manifest")

install("jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38")

And would anyone be kind enough to share the latest pipeline to process EPIC V2 chip methylation data?

Thank you very much.

Zuguang Gu submitted both of those packages as part of the current release, and I submitted a PR for minfi so it will now distinguish the original EPIC from the V2 chip. I don't know if there is a consensus as to what one should do with the individual forward and reverse strand probes however.